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Bio 11 Lecture- Chemistry II

Bio 11 Lecture- Chemistry II. Chemical reactions, Ions, pH, functional groups, organic molecules. What part(s) of an element’s atoms determines its mass?. A. Protons B. Neutrons C. Electrons D. Protons + Neutrons E. Electrons/Protons.

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Bio 11 Lecture- Chemistry II

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  1. Bio 11 Lecture- Chemistry II Chemical reactions, Ions, pH, functional groups, organic molecules

  2. What part(s) of an element’s atoms determines its mass? • A. Protons • B. Neutrons • C. Electrons • D. Protons + Neutrons • E. Electrons/Protons

  3. What part(s) of an element’s atoms define the element? • A. Protons • B. Neutrons • C. Electrons • D. Protons + Neutrons • E. Electrons/Protons

  4. What part(s) of an element’s atoms differentiate its isotopes? • A. Protons • B. Neutrons • C. Electrons • D. Protons + Neutrons • E. Electrons/Protons

  5. What part of atoms determine how they bond with other atoms? • A. Protons • B. Neutrons • C. Electrons • D. Protons + Neutrons • E. Electrons/Protons

  6. Basic atomic structure- protons, neutrons, and electrons

  7. The periodic table logically arranges and describes all matter

  8. Molecules, compounds, chemical reactions, and bonding

  9. Elements combine in chemical reactions to form compounds • Molecules- 2 or more atoms combined in a specific way • Compounds- different elements in a molecule, in exact, whole-number ratios, joined by a chemical bond • 2 major means of intramolecular chemical bonding: Covalent (incl. polar and nonpolar) and Ionic

  10. Valence electrons determine bonding

  11. Atoms seek complete valence electron shells (the octet rule)

  12. In Ionic bonding, atoms strip valence electrons from partners, forming ions

  13. Atoms are stable when their outer shells are filled with electrons • Shell 1: Holds 2 electrons • Shell 2: Holds 8 • Shell 3: Holds 8 • Hydrogen- 1p, 1e, seeks a second electron in its outermost shell • Carbon seeks 4 • The electrons in the outermost shell are called valence electrons

  14. Noble gases have a stable electron structure • Their outer orbitals have a full complement of electrons • Noble gases are very unreactive

  15. LE 2-7 In ionic bonding, an atom takes an electron from another atom, forming 2 ions Transfer of electron Na+ Sodium ion Cl- Chloride ion Sodium chloride (NaCl) Na Sodium atom Cl Chlorine atom

  16. 5. Ions • Ions- Charged atoms or molecules • Anion- negative ion • Cation- positive ion • Ionization- reaction producing ions • Salt- a neutral compound comprised of ions

  17. LE 2-7a-2 Na+ Sodium ion Cl- Chloride ion Sodium chloride (NaCl)

  18. LE 2-7b Na+ Cl-

  19. Water dissolves many ionic compounds (“like dissolves like”) Individual soluble ions are not physically bound to each other

  20. In covalent bonding, pairs of valence electrons are shared, and molecules are formed

  21. LE 2-17a + 2 H2 O2 2 H2O +

  22. LE 2-6b Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8

  23. Structural formula Ball-and-stick model Space-filling model In neutral molecules, carbon always forms 4 bonds Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

  24. LE 3-1b Ethane Propane Carbon skeletons vary in length.

  25. LE 3-1c Butane Isobutane Skeletons may be unbranched or branched. Butane and Isobutane are _______________of each other.

  26. LE 3-1d 1-Butene 2-Butene Skeletons may have double bonds, which can vary in location.

  27. LE 3-1e Cyclohexane Benzene Skeletons may be arranged in rings.

  28. The chemistry of carbon Hydrocarbons are the most basic example Combustible Can form rings Organic Chemistry

  29. The variety of carbon compounds is limitless inorganic - lack carbon atoms organic - with carbon (plus hydrogen) biochemical - organic molecule in life • carbohydrates • proteins • lipids • nucleic acids

  30. Covalent bonds hold together the macromolecules of life • Living things create macromolecular products for structure: • 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g) • Macromolecules as reactants are broken down for energy: C6H12O6(s) + 6O2(g) 6CO2(g)+ 6H2O(l) All the reactions of a living thing are called its metabolism

  31. Electronegativity determines properties of covalently bonded molecules

  32. Electronegativity = “electron greediness” • Atoms in covalently bonded molecules do not always share electrons equally • This creates polar molecules • Polar regions of water molecules interact to form hydrogen bonds • Hydrogen bonds: weak/temporary intermolecular forces

  33. Some electronegativity values • Hydrogen: 2.20 • Oxygen: 3.44 • Carbon: 2.55 • Chlorine: 3.16 • Sodium: 0.93 • Difference between: • H and O: 1.22 • H and C: 0.35

  34. Hydrogen bonding in water determine many of water’s unique properties • H-bonds can form a lattice (ice) • H-bonds require much energy to break • H-bonds give water surface tension Hydrogen bond

  35. Water dissolves many ionic compounds (“like dissolves like”)

  36. 0 Intermolecular Hydrogen bonds give water its surface tension

  37. Intermolecular Hydrogen bonds require much heat in order to be broken

  38. Water also forms ions sometimes H2O ↔ H+ + OH- salt - neutral molecule releases ions acid releases hydrogen H+, burns base releases hydroxide OH–, slimy • Spontaneously happens to water molecules • 1/ 107 water molecules are ionized in distilled water • In dH2O, [H+]= [OH-]

  39. pH is a measure of acidity/basicity • pH = -log [H+] (logarithmic scale) • pH 1 6.9: acid • pH 7.114: base • pH 7 neutral • buffers - absorb excess H+ or OH– • - stomach 2, urine 5-7.8, blood 7.4 • Acids donate [H+] to water • Bases remove [H+] from water (or donate [OH-] to water) • Proteins are very sensitive to small changes in pH

  40. pH scale H+ H+ H+ OH H+ Lemon juice, gastric juice H+ OH H+ H+ H+ Grapefruit juice, soft drink Increasingly ACIDIC (Higher concentration of H+) Acidic solution Tomato juice LE 2-15 Human urine OH OH NEUTRAL [H-] Pure water OH H+ H+ Human blood OH OH H+ H+ H+ Seawater Neutral solution Increasingly BASIC (Lower concentration of H+) Milk of magnesia Household ammonia OH OH OH H+ OH Household bleach OH OH H+ Oven cleaner Basic solution

  41. 7. FUNCTIONAL GROUPS hydroxide group – OH amino group – NH2 carboxyl group – COOH phosphate group – PO4 methyl group – CH3

  42. The physical/ chemical properties of carbon skeletons can be modified by functional groups

  43. figure 02-20b.jpg 2.20 – Part 2 Figure 2.20 – Part 2

  44. Functional groups can radically change the function of a molecule Estradiol Female lion Testosterone Male lion

  45. The six functional groups that are most important in the chemistry of life: • Hydroxyl group (alcohols)* • Carbonyl group • Carboxyl group (carboxylic acids)* • Amino group* • Sulfhydryl group • Phosphate group* • Methyl group

  46. STRUCTURE LE 4-10aa (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Alcohols (their specific names usually end in -ol) Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

  47. Acetone, the simplest ketone EXAMPLE STRUCTURE LE 4-10ab Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

  48. EXAMPLE STRUCTURE LE 4-10ac Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Has acidic properties because it is a source of hydrogen ions. Carboxylic acids, or organic acids The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

  49. EXAMPLE STRUCTURE LE 4-10ba Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Acts as a base; can pick up a proton from the surrounding solution: Amine (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

  50. EXAMPLE STRUCTURE LE 4-10bb (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Thiols

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